Piero Carninci
@carninci
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Biologist @RIKEN, @humantechnopole. Interests: genomics, gene regulation, gene discovery, non-coding RNAs. Other: sports (soccer, etc.). Opinions are my own.
Yokohama, JP & Milan, IT
Joined January 2010
Thrilled to share the review "Long non-coding RNAs: definitions, functions, challenges and recommendations" just published in Nature Reviews Molecular Cell Biology. It was fantastic to be involved with outstanding colleagues to write on lncRNAs!.
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As announced yesterday, I'm thrilled to take a new position as Head of the Functional Genomics programme at the Genomics Research Centre of Human Technopole in Milan. This is one chance in a lifetime to construct a genomics center from scratch.
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1/ Recently I positively re-reviewed a great manuscript, but 1 reviewer (out of 3) was vehemently opposed to publication, with random arguments. I suggested that to the editor that he/she should take independent decisions, excluding unreasonable/unsubstantiated reviews/reviewers.
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1- A key paper from our labs is finally out: This work important because report a methodology: a new approach to globally detect where RNAs interact with chromatin.
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FANTOM papers out in Genome Research! .In the core paper, we show lncRNAs function by knocking down 300 lncRNAs followed by CAGE and imaging analysis. See also transcript recounting and zoo promoterome works.
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Quite a strategic preprint for us in We establish protocols and bioinformatics pipeline using transcription profiling in 10X to essentially reproduce the CAGE results but at single cell: measuring expression mRNAs/lncRNAs, promoter usage and enhancers.
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How many talented dedicated students will be lost until Japan government realizes that it’s important to let students come into the country (after proper vaccination, testing and quarantine). This is much more important than, for instance, professional athletes.
I am withdrawing from the Japan Foundation fellowship. I am heartbroken, but I am done waiting. I am done "hanging in there." 🧵
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Quake:.Which combination of genes are better to define cell types?.Transcription factors define cells better!.Surprisingly: cell surface markers are the worst to predictors of cell types!!.#EMBOsinglecellbio.
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We are looking for the most creative and outstanding colleagues in functional genomics for the Centre of Genomic (Functional Genomics Programme) being established in Milan at the Human Technopole. I appreciate if distributed broadly.
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26 years ago today I landed in Japan for an initial short postdoc. RIKEN was not that well known outside Japan but with the ambition and vision to do big science. I was lucky to join at the right time just before the Genomics Science Center was established.
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A pleasure to receive a nice certificate from the president of RIKEN, Prof Gonokami, thanking for my long service.
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Thrilled to share the efforts lead by @chungchau_hon at @RIKEN_IMS, at atlas of single-cell gene expression in 23 human tissues centered on 5' ends. Want to know how promoters and enhancers are identified in single cells? have a look at the manuscript:
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18 PhD project fully funded positions at the Human Technopole (including my lab). RT appreciated!.
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After quite a bit of work, the single cell blood transcriptomics data of the supercentenarians available under controlled access. Applications forms at the link. The paper is
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Advantages to be in Italy: on a random express train, sitting by chance next to former members of “Alpini” (part of the Italian army) going to Udine for the annual gathering/celebrations. They took out and happily shared salami, various hams, sausages, red and white wine, grappa!
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CAGE at single cell. To specifically detect promoters, enhancers, non-polyA RNAs including lncRNAs. Thanks to all the colleagues pushing hard for this.
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4/ In particular, requests that burn much budget, or would take unreasonable time, or would not add substantial value to the core message, must be avoided. Science cannot be only for wealthy labs. Often papers are linked to a graduation, a promotion, be aware and reasonable.
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After contributing for many years to science in Japan, the news that we do not want to see: Japan science productivity falls at the 10th place for global influential publication ranking. Block/delay of visa for students/researchers will not help.
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E' tempo per essere coinvolti personalmente in una grande scommessa,.
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Finally, finally out! RNAi machinery (AGO1) role in the nucleus to regulate 3D architecture. This links transcribed enhancer to 3D organization, gene expression and role for eRNAs.
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Just written to an Editor in Chief. Wen asking access to data in a paper we were told:. "Thank for your attention! All we can supply are in the supplement materials. Part of the raw data are not available because of intellectual property right. Best wishes!".If so, don't publish!.
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While Omicron is spreading in the country probably arrived with reentrants/US troops, blocking new foreigner entry is only about increasing political consensus: appealing to the guts of ppl, without considerations for what is good for education, science, innovation, business etc.
The government’s policy of blocking new entries by foreigners received 88% support. Its overall performance on COVID-19 was supported by 61%, the most since the question was added in February 2020.
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For those still celebrating the end of 2021, here is the first morning of 2022!
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Group picture from the Human Cell Atlas meeting in Tokoyo, May 23-24. Thanks to everyone for coming here and give us a so great time with big science! #HumanCellAtlas
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Finally out! Congratulations to @JayShin and all colleagues at @RIKEN_IMS @riken_en! By introducing full-length transcription factors (TF) in fibroblasts following by single cells, this work dissects roles of TFs in generating different neuron types.
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Tokyo.
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Rejected a manuscript. Among many other problems: . materials and data will be available "upon reasonable request".
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Transcriptome analysis of supercentenarians (people that love beyond 110 years) reveal expansion of cytotoxic CD4 T cells. The paper is finally out in PNAS!.
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2/ Editors should be strong enough to disagree with unreasonable reviewers, regardless how famous/influential reviewers may be, and exclude them. In particular, poorly substantiated rejections, emotional and angry remarks should be considered unethical reviews and be discarded.
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A kit for the detection of the COVID-19 in only 10~30 minutes was just announced (Japanese press). The kit is based on the SMART-AMP technology developed by Yoshihide Hayashizaki at RIKEN-PMI and implemented by my colleague Kengo Usui at RIKEN-IMS. Thanks!.
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Excellent perspective on genome annotation by @RodericGuigo, envisioning not only genome sequencing of million species but also functional annotation, transcriptome and discusses critical technical issues.
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1/Delighted to share our paper finally out in @CellCellPress, which reports and discusses unexpected recombination mediated by repeat elements in somatic genomes. Details also in the excellent thread of Giovanni Pascarella @muju79,
Beyond ecstatic to share that our paper is finally out @CellCellPress!.It's been a while since I lastly highlighted the main findings, so here's a refresher for new and old readers with some new data added during the peer-review process (-18).
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Cannot agree more. Not only business, but education, research, universities, etc all need new foreign entrants… while omicron is already the dominant variant. Showing that the country is closed to foreigners is just to increase short term political consensus.
Rakuten CEO Mikitani blasts Japan's extended border controls keeping new foreign entrants out until at least the end of February, deeming Kishida's decision "illogical".
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Congratulations to Honjo sensei for the Nobel prize! .Also a reminder that basic science is necessary for future therapies, including cancer.
BREAKING NEWS.The 2018 #NobelPrize in Physiology or Medicine has been awarded jointly to James P. Allison and Tasuku Honjo “for their discovery of cancer therapy by inhibition of negative immune regulation.”
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Dropping accidentally my espresso after learning that Japan is closing its border to non Japanese, again…
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If you win a Nobel Prize, you have better win from an Italian University.
Cori da stadio per il #PremioNobel2021 per la fisica Giorgio Parisi. #sapienza #PremioNobel @SapienzaRoma
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@StrandedOutJPN @ItalyinJPN @arig_airj @humantechnopole Not allowing researchers in Japan has been massively damaging to all the research programs. We have not hired anyone (postdoc, students, other experts) for more than a year @RIKEN_JP @riken_en.
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Great to see the C1 single cell CAGE finally out. CAGE allows profiling capped mRNA expression and simultaneous single-base resolution mapping of their promoters, as well as promoters of lncRNAs and enhancer RNAs. This work.
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Congratulations to authors of the ENCODE papers, finally out! Here we tried to summarize some key aspects, there is much more analysis in each of the papers and more to learn from the produced data.
The third phase of ENCODE delivers an invaluable genomic encyclopedia. For highlights of the.project, this N&V by @chungchau_hon & @carninci is a must-read.
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Hiring postdocs for my new lab at the Human Technopole! Please do carefully elaborate in the motivation letter why you want to join my lab.
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5/ Perhaps all these things are obvious to everyone (they are obvious to me at least), but actually they still affect much of the work. Should ethics in reviewing process be taught? How and where?.
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Good article covering the efforts of a key Italian MD fighting against the anti-vaxxers.
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Looking for outstanding PIs in functional genomics at the Human Technopole in Milan. We develop and broadly apply technologies to study genome regulation, with emphasis on non-coding part of the genome and the role of lncRNAs. Details here:
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Thrilled to organize the 2024 Human Cell Atlas General Meeting in Milan in September/October 2024, including a day at the @humantechnopole. Save the date! .
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Respect for the Russian scientists that have signed a letter against the war in Ukraine, and signed with their name and affiliation. This is not like expressing your opinion in a free country; let's keep keep in mind them, if they many need our help.
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New FANTOM6 effort to annotate putative function of lncRNAs, based on genomic interaction maps, RNA binding protein data and RNA interaction data. Comments and suggestions welcome! .
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A brief correspondence in Nature, suggesting reforms needed to boost Japanese science. Diversity needed, not conformity. Concerns shared by many more colleagues, including top Japanese scientist.
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Skiing, to forget. From Shiga Kogen today one could see I’d say half Japan. The North Japanese Alps, far away (zoom in).
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Save a tree. Do not buy Obokata's book telling it's someone else fault. There is no conspiracy.
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@FichotVincent Admiration and respect for your battle. Happy to see results. I lost a similar war long time ago, never seeing my first daughter after October 2008.
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3/ As reviewers, we all should consider that the main purpose of reviewing is to publish reasonable papers, not preventing their publication at any cost; of course unless there are flaws or real issues that need to be addressed or solved. Often MS are very good!.
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I’ve tried to provide a summary of genome regulation and noncoding-RNAs function and perspectives, in Italian. So difficult. Ho provato a spiegare in italiano cosa fa il genoma, in particolare la parte non codificante proteine, comprese prospettive future.
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Xiang-Dong Fu. The genome is coated with RNA binding proteins, including 70% of promoters. Other studies (including ours) suggest that the genome is also coated with RNAs, therefore do we need to broadly reconsider how chromatin is made and regulated? .#KSlncRNA.
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Pandora-seq: capturing all the small RNAs by removing modifications that usually prevent ligation and sequencing, reveals a new landscape including tsRNAs and rsRNAs; miRNA not the only/main class of small RNAs. Interesting thread.
Now alive! We develop PANDORA-seq @NatureCellBio to overcome RNA modifications that prevent small RNA detection in traditional RNA-seq, uncovering a new small RNA landscape that is in fact dominated by tsRNA/rsRNA, rather than miRNA in many tissues/cells👇.
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90% drop of foreign students is severe, will cause long term consequences for the system. Must fix immediately.
This is really sad and disappointing and has most likely affected the lives of thousands of people.
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One of the largest NMR structure of a lncRNA domain determined so far is out, and is a SINEUP domain of 167 nt!.This was a long technical marathon: we used NMR ‘fingerprints’ as sensitive probe to survey domains before determining fine structures.
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Annual ceremony today at @riken_yokohama to remember and thank the animals sacrificed for experiments. Their sacrifice is needed for research and ultimately to develop new drugs and treatments.
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There are times when everything seems hard. Then, two former interns write me; one to say thanks because the internship in my lab was instrumental for her job in a biotech. And the other, who was inspired by the internship to enter grad school and get his PhD. Yes it was useful!.
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Railway in the direction of mount Fuji- Kanagawa, Yokohama-line near Kamoi, taken at 6:30 AM, early morning cycling.
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Reciprocity of travel conditions between EU and Japan. Not only a human right for families separated by the pandemic but also in the interest of business, research, innovation. Time to push harder please.
Insightful roundtables with 🇪🇺 & 🇯🇵 companies based in Tokyo. In order to grow, companies of all sizes & sectors must benefit from the same rules, whether they are in Japan or Europe. We need to ensure #reciprocity, including lifting current travel restrictions for 🇪🇺 citizens.
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@EricTopol Systematic use of masks, partial lockdowns until vaccines became available, reopening slowly and still recommending masks. PCR tests were too few at the beginning but this is unrelated to deaths. The pandemic was not a political issue.
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Smart-Amp (スマートアンプ), developed by Usui, Hayashizaki and colleagues at RIKEN to detect the SARS-COV-2, to be available from tomorrow for diagnosis in Kanagawa prefecture. I hope this can help to overcome the lack of testing in Japan.
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Japanese posts are amazing. This was delivered correctly to me in Yokohama (not in Saitama).
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The protocols of the Human Cell Atlas are grouped here: We hope that this will help to distribute standardized protocols to the community!.@humancellatlas #HumanCellAtlas.
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Excited to announce the EMBO Single Cell Biology we are organizing in Tokyo, May 20-22. Registrations are open, see the speakers lineup: looking forward to see many of you at the meeting!.
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Improved CAGE protocol, low quantity (50ng~), 96 weels format,simplified, No-PCR. Useful for large scale perturbations assays, to measure promoters, enhancers, lncRNAs.
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The last day of Aki Minoda at Riken, starting her new lab at Radboud University in The Netherlands. We hired her at RIKEN as junior PI 9 years ago, promoted eventually to full PI,. but time to move on, we will continue to collaborate for the mouse aging atlas and it’s “regulome”.
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Telling a lab member that I was reading lots of papers when working to develop the technologies for the FANTOM Project and then for the interpretation of transcriptome data. How many?. I do not know, but here is the collections of the folders (@ Yokohama’s office).
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The Human Cell Atlas, Asia meeting, starting now in Kolkata, India. Fantastic work by Partha Majumder and his team, amazing organization. Huge progress of this community since the first HCA Asian meeting in 2017. @humancellatlas
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Wow: a lncRNA corrects a classic metabolic disease, phenylketonuria, interacting with the key enzyme phenylalanine hydroxylase (PAH): HULC lncRNA potentiates phenylalanine metabolism in mice.
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Unusual jelly fish invasion in Trieste. Tempted to give some title to these pics like “crowded academic field” or “competition in the fast track science”, or “welcoming new researchers in a crowded field”. I’m sure @OdedRechavi can do better.
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A top university, Kobe U., cancelling a semester for international/exchange students. Apart the dramatic impact on students, this reverts the internationalization of universities, impacting future research, development, business etc. It’s a big damage for Japan as well.
[BREAKING] Kobe University @KobeU_Global, one of the highest ranking national universities in Japan, is cancelling the FALL SEMESTER for exchange/intl students. "It is unlikely that the borders will be open (. ) for the Fall semester". Source: a student from our community.
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Taking new challenges as Deputy Center Director of the new IMS, the RIKEN Center for Integrative Medical Sciences. In particular, I will work to bring together human genetics and genomics, but also looking at the Immunology and other research fields.
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Looking for a group leader in functional genomics with focus on computational biology. See details at:
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It seems yesterday that we launched the FANTOM Consortium to annotate mammalian genes. Many episodes, brainstorms, unexpected discoveries and 20 years later, open genomics data are still essential for many colleagues. Find here the updated FANTOM database!.
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Many RNAs interact with chromatin, likely specific, often functionally, yet we lack comprehensive RNA-chromatin maps. We posted the ms "RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions" on Biorxiv.
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It seems yesterday, 20 years ago today, when we kicked off the FANTOM1. Many came from abroad to become fantastic collaborators and friends of a long scientific adventure. Most of them stayed for 2 weeks discussing how to "ANNOTATE" 20,000 mouse full-length cDNA.
The first FANTOM meeting was held from August 28, 2000. Thus, today is the 20th anniversary of the FANTOM project!. Thank you for your continued interests and supports to FANTOM.
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Delighted to see this out. The work deepens our understanding of lncRNAs structure-function relationships, ultimately suggesting that RNAs functional element deriving from SINE may acquire similar folding and function, even without shared ancestor.
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Human Technopole organizing a single cell workshop in September. Save the date.
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Happy to see the out at @genomeresearch. We have been exploring the cap-trapper technology to sequence both long and short cap-selected (full-length) RNAs, including longer reads, using THP-1 cells stimulated with PMA. Unsurprisingly, we found new RNAs.
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Some suggestion at the Gordon conference, for those suffering impostor syndrome. Apparently many in science.
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Congratulations to Aviv Regev for the Keio Medical Science Prize for development of the single cell genomics field. Very well deserved!.@humancellatlas .
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Happy 2023, this is how it looks like from Yokohama right now. I added also some early plum blossoms.
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Merry Christmas, with some morning/evening colors and lights.
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あけましておめでとう御座います🎊. Happy new year. Buon Anno Nuovo!.This new year looks promising, starting with a bright, beautiful day. Let’s hope that we will get back to normal!
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Beautiful model of management of the COVID-19 pandemic in Japan in the past 18 months; increased infectiousness (Ro) shown with steeper slope, vaccination reduces the slope. Lockdowns act as a breaks, GoTo campaigns (support from government to travel, dine etc) as accelerators.
リクエストがあったので変異株でR0が変化する効果も追加。R0=2.5(original), 3(EU), 4(α), 6.5 (δ)を適当に直線補完。ワクチンの感染防止率を60%と仮定。いろいろ仮定しての可視化なのでただの「考え方」。 @mansai4 @carninci
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March 28 is the day when I landed in Japan, 23 years ago, for a postdoc. I just knew I wanted to prove myself in the lab, develop technologies to analyze the genome. Frankly I did not make any long term plan apart from pushing: there was no job back in Italy. Desperation helped.
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Interested in getting a PhD in Italy with the SEMM program (which included the Human Technopole)? See details here. The program is actually very good. We welcome international applicants.
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I’ll continue to tweet this type of information until we will see the children kidnapping problem in Japan solved. Thanks to @FichotVincent for this battle, which is not only a problem of foreigners.
BBC japan.
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Jay Shin. Expanding the FANTOM5 promoter/enhancers etc. maps to any single cell? Presenting the protocols that can do this and data (example: "bidirectional enhancers" are unidirectional in each single cell). #hcaasia2019.
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The most interesting espresso I’ve received recently, but I think that today I can cope with this.
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Looking urgently for either a postdoc or a technical staff (with good understanding of single cell and genomics/next generation sequencing technologies) for a @cziscience grant for technical development, particularly to standardize single-cell CAGE.
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The position is back on the web site: :.Looking for outstanding candidates for a group leader position in computational biology for the Centre of Genomics, Functional Genomics Program. Re-posting appreciated!.
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